Jeffrey F. Harper's research while affiliated with University of Nevada, Reno and other places
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Publications (158)
During angiosperm sexual reproduction, pollen tubes must penetrate through multiple cell types in the pistil to mediate successful fertilization. Although this process is highly choreographed and requires complex chemical and mechanical signaling to guide the pollen tube to its destination, aspects of our understanding of pollen tube penetration th...
Calcium ion transporting systems control cytosol Ca2+ levels ([Ca2+]cyt) and generate transient calcium (Ca2+) signatures that are key to environmental responses. Here, we report an impact of resting [Ca2+]cyt on plants from the functional study of calmodulin-regulated Ca2+ pumps or Ca2+-ATPases in Arabidopsis (Arabidopsis thaliana). The plasma mem...
A potential strategy to mitigate oxidative damage in plants is to increase the abundance of antioxidants, such as ascorbate (i.e., vitamin C). In Arabidopsis (Arabidopsis thaliana), a rate limiting step in ascorbate biosynthesis is a phosphorylase encoded by Vitamin C Defective 2 (VTC2). To specifically overexpress VTC2 (VTC2 OE) in pollen, the cod...
Ethiopian mustard (Brassica carinata) is an ancient crop with remarkable stress resilience and a desirable seed fatty acid profile for biofuel uses. B. carinata is one of six Brassica species that share three major genomes from three diploid species (AA, BB, and CC) that spontaneously hybridized in a pairwise manner to form three allotetraploid spe...
Atmospheric elemental mercury (Hg(0)) enters plant stomata, becomes oxidized, and is then transferred to annual growth rings providing an archive of air Hg(0) concentrations. To better understand the processes of Hg accumulation and translocation, the foliage of quaking aspen and Austrian pine were exposed to Hg(0) in the air, and methylmercury (Me...
Ethiopian mustard (Brassica carinata) is an ancient crop with significant potential for expanded cultivation as a biodiesel feedstock. The remarkable stress resilience of B. carinata and desirable seed fatty acid profile addresses the ongoing food vs. fuel debate as the crop is productive on marginal lands otherwise not suitable for even closely re...
Land plants evolved to quickly sense and adapt to temperature changes, such as hot days and cold nights. Given that calcium (Ca ²⁺ ) signaling networks are implicated in most abiotic stress responses, heat-triggered changes in cytosolic Ca ²⁺ were investigated in Arabidopsis leaves and pollen. Plants were engineered with a reporter called CGf, a ra...
Sexual reproduction in flowering plants takes place without an aqueous environment. Sperm are carried by pollen through air to reach the female gametophyte, though the molecular basis underlying the protective strategy of the male gametophyte is poorly understood. Here we compared the published transcriptomes of Arabidopsis thaliana pollen, and of...
![OnGuard3 predicts an elevation in [Ca²⁺]i on steps to 1,000 μbar CO2...](publication/353571229/figure/fig3/AS:1051146890248192@1627624356045/OnGuard3-predicts-an-elevation-in-Cai-on-steps-to-1-000mbar-CO2-and-an-undershoot-in_Q320.jpg)
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Stomata of most plants close to preserve water when the demand for CO2 by photosynthesis is reduced. Stomatal responses are slow compared with photosynthesis, and this kinetic difference erodes assimilation and water-use efficiency under fluctuating light. Despite a deep knowledge of guard cells that regulate the stoma, efforts to enhance stomatal...
Thiamin and thiamin pyrophosphate (TPP) are essential components for the function of enzymes involved in the metabolism of carbohydrates and amino acids in living organisms. In addition to its role as a cofactor, thiamin plays a key role in resistance against biotic and abiotic stresses in plants. Most of the studies used exogenous thiamin to enhan...
Climate change has created an environment where heat stress conditions are becoming more frequent as temperatures continue to raise in crop production areas around the world. This situation leads to decreased crop production due to plant sensitivity to heat stress. Reproductive success is critically dependent on plants’ ability to produce functiona...
Being around for several decades, there is a vast amount of academic research on biomining, and yet it contributes less to the mining industry compared to other conventional technologies. This critique briefly comments on the current status of biomining research, enumerates a number of primary challenges, and elaborates on some kinetically-oriented...
Generating cellular Ca2+ signals requires coordinated transport activities from both Ca2+ influx and efflux pathways. In Arabidopsis (Arabidopsis thaliana), multiple efflux pathways exist, some of which involve Ca2+-pumps belonging to the Autoinhibited Ca2+-ATPase (ACA) family. Here we show that ACA1, 2, and 7 localize to the endoplasmic reticulum...
Climate change has created an environment where heat stress conditions are becoming more frequent as temperatures continue to rise in crop production areas around the world. This situation leads to decreased crop production due to plant sensitivity to heat stress. Reproductive success is critically dependent on plants' ability to produce functional...
The lipid bilayer of biological membranes has a complex composition, including high chemical heterogeneity, the presence of nanodomains of specific lipids, and asymmetry with respect to lipid composition between the two membrane leaflets. In membrane trafficking, membrane vesicles constantly bud off from one membrane compartment and fuse with anoth...
During sexual reproduction in flowering plants, pollen grains germinate on the stigma surface and grow through the stigma-style tissue to reach the ovary and deliver sperm cells for fertilization. Here, we outline a method to test whether a pollen fertility mutation specifically disrupts pollen penetration through the stigma-style barrier. This met...
Aminophospholipid ATPases (ALAs) are lipid flippases involved in transporting specific lipids across membrane bilayers. Arabidopsis thaliana contains 12 ALAs in five phylogenetic clusters, including four in cluster 3 (ALA4, -5, -6, and -7). ALA4/5 and ALA6/7 are expressed primarily in vegetative tissues and pollen, respectively. Previously, a doubl...
In flowering plants, pollen tubes undergo tip growth to deliver two nonmotile sperm to the ovule where they fuse with an egg and central cell to achieve double fertilization. This extended journey involves rapid growth and changes in gene activity that manage compatible interactions with at least seven different cell types. Nearly half of the genom...
Background:
In flowering plants, the male gametophyte (pollen) is one of the most vulnerable cells to temperature stress. In Arabidopsis thaliana, a pollen-specific Cyclic Nucleotide-Gated cation Channel 16 (cngc16), is required for plant reproduction under temperature-stress conditions. Plants harboring a cncg16 knockout are nearly sterile under...
During pollen-pistil interactions in angiosperms, the male gametophyte (pollen) germinates to produce a pollen tube. To fertilize ovules located within the female pistil, the pollen tube must physically penetrate specialized tissues. Whereas the process of pollen tube penetration through the pistil has been anatomically well-described, the genetic...
Protein phosphorylation regulates numerous cellular processes. Identifying the substrates and protein kinases involved is vital to understand how these important post-translational modifications modulate biological function in eukaryotic cells. Pyrophosphatases catalyse the hydrolysis of PPi to Pi, driving biosynthetic reactions; they are essential...
Plants show a rapid systemic response to a wide range of environmental stresses, where the signals from the site of stimulus perception are transmitted to distal organs to elicit plant-wide responses. A wide range of signaling molecules are trafficked through the plant, but a trio of potentially interacting messengers, reactive oxygen species (ROS)...
Plants use solar energy to produce lipids directly from inorganic elements and are not thought to require molecular systems for lipid uptake from the environment. Here we show that Arabidopsis thaliana Aminophospholipid ATPase10 (ALA10) is a P4-type ATPase flippase that internalizes exogenous phospholipids across the plasma membrane, after which th...
Members of the P4 subfamily of P-type ATPases are thought to create and maintain lipid asymmetry in biological membranes by flipping specific lipids between membrane leaflets. In Arabidopsis, 7 of the 12 Aminophospholipid ATPase (ALA) family members are expressed in pollen. Here we show that double knockout of ALA6 and ALA7 (ala6/7) results in sili...
Plant auto-inhibited Ca2+-ATPases (ACA) are crucial in defining the shape of calcium transients and therefore in eliciting plant responses to various stimuli. Arabidopsis
thaliana genome encodes ten ACA isoforms that can be divided into four clusters based on gene structure and sequence homology. While isoforms from clusters 1, 2 and 4 have been ch...
Several pollen-specific motifs are present in the intergenic region immediately upstream of ALA3. Sequence data was obtained from The Arabidopsis Information Resource (www.arabidopsis.org) and reads in the 5′ → 3′ direction. Putative conserved regulatory elements were found using the PLACE (A Database of Plant Cis-Acting Regulatory DNA Elements) we...
Cytoplasmic streaming is disorganized in ala3 pollen tubes. Images for this example were taken using DIC microscopy at regular intervals of ∼0.6 s over a 1 m time period. Movie plays at ∼10× speed.
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Cytoplasmic streaming in wild-type pollen tubes. Images for this example were taken using DIC microscopy at regular intervals of ∼0.6 s over a 1 m time period. Movie plays at ∼10× speed.
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PCR primers used to genotype ala3 T-DNA insertion lines. Sequences read in the 5′ → 3′ direction. Lowercase letters in 684a represent introduced restriction sites used for subcloning.
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Elemental concentrations in leaf tissue are not significantly different in ala3 and wild-type. Average results (±SE) for 3–6 independent experiments (n≥20 plants for each genotype) are presented for wild-type (open bars), ala3-1 (checkered bars), ala3-4 (gray bars), and ala3 plants rescued by the expression of full length ALA3 (crosshatched bars)....
Concentrations of 144 lipids in ala3 and wild-type pollen. This data is summarized in Figure 7. Lipid concentrations were measured using tandem mass spectrometry (MS/MS) that detected 11 different head-groups and quantified the acyl carbons and double bonds within the corresponding acyl side chain(s). Concentrations are expressed as a percentage of...
Members of the P4 subfamily of P-type ATPases are thought to help create asymmetry in lipid bilayers by flipping specific lipids between the leaflets of a membrane. This asymmetry is believed to be central to the formation of vesicles in the secretory and endocytic pathways. In Arabidopsis thaliana, a P4-ATPase associated with the trans-Golgi netwo...
Gene expression is altered in abh1 mutant plants. Data represents the smallest fold change in gene expression between abh1 and wild-type from two biological replicates. Microarray data used for this analysis is publicly available in the NCBI GEO database (http://www.ncbi.nlm.nih.gov/projects/geo/, GSE7112) and was originally published by Kuhn et al...
75 mM NaCl soil modification does not alter Col-0 seed size. Average results (±SE) of four independent experiments are presented for untreated (open bars, n = 12 plants) and 75 mM NaCl (crosshatched bars, n = 12 plants) soil conditions. Seed sizes were measured from scanned images as two-dimensional areas using the ImageJ software package. No stati...
Elemental abundances in vegetative tissue. The elemental contents of mutant plants relative to the tray average is represented in terms of z-Scores (number of standard deviations from the tray mean). Data represents the median z-Scores of an experimental line within an individual flat. Boxes shaded in gray represent circumstances for which no data...
Cumulative results of trace element screen. The concentrations of elements in experimental plants relative to the Col-0 controls are represented in terms of z-Scores (number of standard deviations from the control mean). Data represents the median z-Scores of an experimental line within an individual flat. Boxes shaded in gray represent circumstanc...
Gene ontology analyses comparing genes with potential phenotypes to genes without potential phenotypes. Analyses were done as described in Figure S2. Genes were considered to have a potential ionomic phenotype if they were identified as candidates in the first pass screen. Eight of the 760 genes screened were not included in the GO analysis because...
The concentrations of mineral nutrients in seeds are critical to both the life cycle of plants as well as human nutrition. These concentrations are strongly influenced by soil conditions, as shown here by quantifying the concentration of 14 elements in seeds from Arabidopsis thaliana plants grown under four different soil conditions: standard, or m...
Gene ontology analyses comparing the genes from the mutant screen to the A. thaliana genome. Gene Ontology (GO) analyses were done using gene ontology annotations from TAIR (http://www.arabidopsis.org). Three aspects of each gene product are considered individually: biological process, cellular component and molecular function. Each aspect is divid...
Primers used in this study.
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DNA sequences of plasmid constructs used in this study.
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Sequence alignment of cyclic nucleotide binding domains (CNBDs) from CNGCs.
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Seed stocks used in this study.
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The Arabidopsis thaliana genome contains 20 CNGCs, which are proposed to encode cyclic nucleotide gated, non-selective, Ca(2+)-permeable ion channels. CNGC7 and CNGC8 are the two most similar with 74% protein sequence identity, and both genes are preferentially expressed in pollen. Two independent loss-of-function T-DNA insertions were identified f...
Cyclic nucleotide-gated channels (CNGCs) have been implicated in diverse aspects of plant growth and development, including responses to biotic and abiotic stress, as well as pollen tube growth and fertility. Here, genetic evidence identifies CNGC16 in Arabidopsis (Arabidopsis thaliana) as critical for pollen fertility under conditions of heat stre...
Although calcium-dependent protein kinases (CDPKs or CPKs) are classified as serine/threonine protein kinases, autophosphorylation on tyrosine residues was observed for soybean CDPKβ and several Arabidopsis isoforms (AtCPK4 and AtCPK34). We identified Ser-8, Thr-17, Tyr-24 (in the kinase domain), Ser-304, and Ser-358 as autophosphorylation sites of...
Five organisms having completely sequenced genomes and belonging to all major branches of green plants (Viridiplantae) were analyzed with respect to their content of P-type ATPases encoding genes. These were the chlorophytes Ostreococcus tauri and Chlamydomonas reinhardtii, and the streptophytes Physcomitrella patens (a non-vascular moss), Selagine...
Diminished Na,K-ATPase expression has been reported in several carcinomas and has been linked to tumor progression. However, few studies have determined whether Na,K-ATPase function and expression are altered in lung malignancies. Because cigarette smoke (CS) is a major factor underlying lung carcinogenesis and progression, we investigated whether...
The identification of substrates represents a critical challenge for understanding any protein kinase-based signal transduction pathway. In Arabidopsis, there are more than 1000 different protein kinases, 34 of which belong to a family of Ca(2+)-dependent protein kinases (CPKs). While CPKs are implicated in regulating diverse aspects of plant biolo...
Peptides tested in SPA assays. Each peptide was made with norleucine substitutions for methionines (except ach-375), and a biotin tag on the N-terminal end.
Sequences of plasmids used in this study.
The cytoplasmic Ca(2+) signals that participate in nearly all aspects of plant growth and development encode information as binary switches or information-rich signatures. They are the result of influx (thermodynamically passive) and efflux (thermodynamically active) activities mediated by membrane transport proteins. On the influx side, confirming...
Calcium (Ca(2+)) signals regulate many aspects of plant development, including a programmed cell death pathway that protects plants from pathogens (hypersensitive response). Cytosolic Ca(2+) signals result from a combined action of Ca(2+) influx through channels and Ca(2+) efflux through pumps and cotransporters. Plants utilize calmodulin-activated...
Results of in silico experimental design simulations. A. Number of QTLs detected in the subset of CviLer lines with 3 samples analyzed. First two rows indicate the average of 10 randomly generated subsets with n = 1 or 2, third row indicates the number of QTLs identified with the full n = 3 dataset. B. QTLs identified from the large BaySha experime...
All QTL for each element across all 5 RIL populations. LOD (logarithm of the odds) score above the LOD threshold is indicated for each QTL. QTL region are indicated by MI start and MI end and the projected QTL location is given in cM. Cofactors indicates the number of cofactors used in the CIM model. Threshold values indicate the 99% confidence int...
Two-way epistatic interactions for each RIL population across all 5 chromosomes. Lod.full is the log-odds ratio of the full model with two loci and their interaction compared to the null model with no QTL. Lod.fv1 is the log-odds ratio of the full model compared to the best single QTL model with one locus on either chromosome A or B (not necessaril...
Frequency plots of parental lines and RILs for each element across the 5 RIL populations. X-axis represents the centered PPM (See Methods) of indicated element. Y-axis indicates frequency of occurrence. Black vertical lines indicate the 95% confidence interval of the parents distribution (i.e. lower parent−1.96 SD (pooled) to higher parent+1.96 SD(...
Frequency plots of parental lines and RILs for each element across the 5 RIL populations. X-axis represents the centered PPM (See Methods) of indicated element. Y-axis indicates frequency of occurrence. Black vertical lines indicate the 95% confidence interval of the parents distribution (i.e. lower parent−1.96 SD (pooled) to higher parent+1.96 SD(...
Significant pairwise comparisons between 12 accessions of A. thaliana. Line effect indicates significant differences (p<0.05) between accessions for that element. A. A. thaliana leaf data. B. A. thaliana seed data.
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Controlling elemental composition is critical for plant growth and development as well as the nutrition of humans who utilize plants for food. Uncovering the genetic architecture underlying mineral ion homeostasis in plants is a critical first step towards understanding the biochemical networks that regulate a plant's elemental composition (ionome)...
Frequency plots of parental lines and RILs for each element across the 5 RIL populations. X-axis represents the centered PPM (See Methods) of indicated element. Y-axis indicates frequency of occurrence. Black vertical lines indicate the 95% confidence interval of the parents distribution (i.e. lower parent−1.96 SD (pooled) to higher parent+1.96 SD(...
Frequency plots of parental lines and RILs for each element across the 5 RIL populations. X-axis represents the centered PPM (See Methods) of indicated element. Y-axis indicates frequency of occurrence. Black vertical lines indicate the 95% confidence interval of the parents distribution (i.e. lower parent−1.96 SD (pooled) to higher parent+1.96 SD(...
Estimated genetic maps. Estimated genetic maps using marker data for our RIL populations in QTL Cartographer display. Map function and unit of measurement are included at the top of each map estimate followed by number of chromosomes, total number of markers mapped, mean and standard deviation for markers and inter-marker distance. The table is a r...
Frequency plots of parental lines and RILs for each element across the 5 RIL populations. X-axis represents the centered PPM (See Methods) of indicated element. Y-axis indicates frequency of occurrence. Black vertical lines indicate the 95% confidence interval of the parents distribution (i.e. lower parent−1.96 SD (pooled) to higher parent+1.96 SD(...
Hoaglands Media Recipe. Modified Hoaglands media used in this study.
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